MCL coexpression mm9:909: Difference between revisions
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{{MCL_coexpression_mm9 | 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regulation of type IV hypersensitivity;0.0112754494454306;20737!GO:0002710;negative regulation of T cell mediated immunity;0.0112754494454306;20737!GO:0001807;regulation of type IV hypersensitivity;0.0112754494454306;20737!GO:0001806;type IV hypersensitivity;0.0112754494454306;20737!GO:0008367;bacterial binding;0.0112754494454306;20737!GO:0002704;negative regulation of leukocyte mediated immunity;0.0112754494454306;20737!GO:0002865;negative regulation of acute inflammatory response to antigenic stimulus;0.0112754494454306;20737!GO:0050688;regulation of defense response to virus;0.0112754494454306;20737!GO:0002862;negative regulation of inflammatory response to antigenic stimulus;0.0112754494454306;20737!GO:0002884;negative regulation of hypersensitivity;0.0112754494454306;20737!GO:0002674;negative regulation of acute inflammatory response;0.0112754494454306;20737!GO:0002707;negative regulation of lymphocyte mediated immunity;0.0112754494454306;20737!GO:0002698;negative regulation of immune effector process;0.014495417890902;20737!GO:0001562;response to protozoan;0.014495417890902;20737!GO:0002709;regulation of T cell mediated immunity;0.0169057622049432;20737!GO:0042535;positive regulation of tumor necrosis factor biosynthetic process;0.0169057622049432;20737!GO:0031254;trailing edge;0.0169057622049432;20737!GO:0002820;negative regulation of adaptive immune response;0.0169057622049432;20737!GO:0001931;uropod;0.0169057622049432;20737!GO:0002823;negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains;0.0169057622049432;20737!GO:0042534;regulation of tumor necrosis factor biosynthetic process;0.0169057622049432;20737!GO:0050777;negative regulation of immune response;0.0169057622049432;20737!GO:0002683;negative regulation of immune system process;0.0169057622049432;20737!GO:0042533;tumor necrosis factor biosynthetic process;0.0169057622049432;20737!GO:0031294;lymphocyte costimulation;0.0186505461425434;20737!GO:0045060;negative thymic T cell selection;0.0186505461425434;20737!GO:0002456;T cell mediated immunity;0.0186505461425434;20737!GO:0043383;negative T cell selection;0.0186505461425434;20737!GO:0031295;T cell costimulation;0.0186505461425434;20737!GO:0051607;defense response to virus;0.0202802464374892;20737!GO:0031348;negative regulation of defense response;0.0213406109698887;20737!GO:0050728;negative regulation of inflammatory response;0.0213406109698887;20737!GO:0002883;regulation of hypersensitivity;0.0213406109698887;20737!GO:0002673;regulation of acute inflammatory response;0.0213406109698887;20737!GO:0002438;acute inflammatory response to antigenic stimulus;0.0213406109698887;20737!GO:0002864;regulation of acute inflammatory response to antigenic stimulus;0.0213406109698887;20737!GO:0002524;hypersensitivity;0.0213406109698887;20737!GO:0000299;integral to membrane of membrane fraction;0.0213406109698887;78885!GO:0007162;negative regulation of cell adhesion;0.0219975137052059;20737!GO:0042130;negative regulation of T cell proliferation;0.0219975137052059;20737!GO:0002861;regulation of inflammatory response to antigenic stimulus;0.0219975137052059;20737!GO:0002437;inflammatory response to antigenic stimulus;0.0219975137052059;20737!GO:0045061;thymic T cell selection;0.0219975137052059;20737!GO:0032640;tumor necrosis factor production;0.0230305870421663;20737!GO:0045058;T cell selection;0.024429934716648;20737!GO:0002703;regulation of leukocyte mediated immunity;0.024429934716648;20737!GO:0002706;regulation of lymphocyte mediated immunity;0.024429934716648;20737!GO:0050868;negative regulation of T cell activation;0.0246732476426524;20737!GO:0008624;induction of apoptosis by extracellular signals;0.0246732476426524;20737!GO:0002697;regulation of immune effector process;0.0246732476426524;20737!GO:0050672;negative regulation of lymphocyte proliferation;0.0246732476426524;20737!GO:0032945;negative regulation of mononuclear cell proliferation;0.0246732476426524;20737!GO:0002819;regulation of adaptive immune response;0.027501868906009;20737!GO:0002822;regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.;0.027501868906009;20737!GO:0033077;T cell differentiation in the thymus;0.0301260709408571;20737!GO:0051250;negative regulation of lymphocyte activation;0.0301260709408571;20737!GO:0042102;positive regulation of T cell proliferation;0.0319583419061254;20737!GO:0031347;regulation of defense response;0.0326021990965578;20737!GO:0051241;negative regulation of multicellular organismal process;0.0326021990965578;20737!GO:0050727;regulation of inflammatory response;0.0326021990965578;20737!GO:0042108;positive regulation of cytokine biosynthetic process;0.0353734580124094;20737!GO:0032946;positive regulation of mononuclear cell proliferation;0.0385149164805372;20737!GO:0050671;positive regulation of lymphocyte proliferation;0.0385149164805372;20737!GO:0045727;positive regulation of translation;0.0421072289428701;20737!GO:0042129;regulation of T cell proliferation;0.0432242556945791;20737!GO:0050870;positive regulation of T cell activation;0.0432242556945791;20737!GO:0031328;positive regulation of cellular biosynthetic process;0.0432242556945791;20737!GO:0048583;regulation of response to stimulus;0.0435742622990178;20737!GO:0030155;regulation of cell adhesion;0.0439139104015371;20737!GO:0009615;response to virus;0.0471136079639364;20737!GO:0042035;regulation of cytokine biosynthetic process;0.0473928022269503;20737!GO:0050670;regulation of lymphocyte proliferation;0.0481839177904082;20737!GO:0032944;regulation of mononuclear cell proliferation;0.0481839177904082;20737!GO:0009891;positive regulation of biosynthetic process;0.0481839177904082;20737!GO:0042098;T cell proliferation;0.0486756628513152;20737!GO:0005625;soluble 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| |||
| | |||
}} | |||
Latest revision as of 16:05, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:62272200..62272221,- | p11@Ncor1 |
| Mm9::chr16:4679660..4679699,- | p2@Coro7 |
| Mm9::chr2:155805181..155805202,- | p@chr2:155805181..155805202 - |
| Mm9::chr7:134281321..134281341,- | p1@Spn |
| Mm9::chr7:150191554..150191578,+ | p2@Tspan32 |
| Mm9::chr7:82731110..82731121,+ | p@chr7:82731110..82731121 + |
| Mm9::chr7:82731147..82731158,+ | p@chr7:82731147..82731158 + |
| Mm9::chr8:114060166..114060201,+ | p2@Znrf1 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0001808 | negative regulation of type IV hypersensitivity | 0.0112754494454306 |
| GO:0002710 | negative regulation of T cell mediated immunity | 0.0112754494454306 |
| GO:0001807 | regulation of type IV hypersensitivity | 0.0112754494454306 |
| GO:0001806 | type IV hypersensitivity | 0.0112754494454306 |
| GO:0008367 | bacterial binding | 0.0112754494454306 |
| GO:0002704 | negative regulation of leukocyte mediated immunity | 0.0112754494454306 |
| GO:0002865 | negative regulation of acute inflammatory response to antigenic stimulus | 0.0112754494454306 |
| GO:0050688 | regulation of defense response to virus | 0.0112754494454306 |
| GO:0002862 | negative regulation of inflammatory response to antigenic stimulus | 0.0112754494454306 |
| GO:0002884 | negative regulation of hypersensitivity | 0.0112754494454306 |
| GO:0002674 | negative regulation of acute inflammatory response | 0.0112754494454306 |
| GO:0002707 | negative regulation of lymphocyte mediated immunity | 0.0112754494454306 |
| GO:0002698 | negative regulation of immune effector process | 0.014495417890902 |
| GO:0001562 | response to protozoan | 0.014495417890902 |
| GO:0002709 | regulation of T cell mediated immunity | 0.0169057622049432 |
| GO:0042535 | positive regulation of tumor necrosis factor biosynthetic process | 0.0169057622049432 |
| GO:0031254 | trailing edge | 0.0169057622049432 |
| GO:0002820 | negative regulation of adaptive immune response | 0.0169057622049432 |
| GO:0001931 | uropod | 0.0169057622049432 |
| GO:0002823 | negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0169057622049432 |
| GO:0042534 | regulation of tumor necrosis factor biosynthetic process | 0.0169057622049432 |
| GO:0050777 | negative regulation of immune response | 0.0169057622049432 |
| GO:0002683 | negative regulation of immune system process | 0.0169057622049432 |
| GO:0042533 | tumor necrosis factor biosynthetic process | 0.0169057622049432 |
| GO:0031294 | lymphocyte costimulation | 0.0186505461425434 |
| GO:0045060 | negative thymic T cell selection | 0.0186505461425434 |
| GO:0002456 | T cell mediated immunity | 0.0186505461425434 |
| GO:0043383 | negative T cell selection | 0.0186505461425434 |
| GO:0031295 | T cell costimulation | 0.0186505461425434 |
| GO:0051607 | defense response to virus | 0.0202802464374892 |
| GO:0031348 | negative regulation of defense response | 0.0213406109698887 |
| GO:0050728 | negative regulation of inflammatory response | 0.0213406109698887 |
| GO:0002883 | regulation of hypersensitivity | 0.0213406109698887 |
| GO:0002673 | regulation of acute inflammatory response | 0.0213406109698887 |
| GO:0002438 | acute inflammatory response to antigenic stimulus | 0.0213406109698887 |
| GO:0002864 | regulation of acute inflammatory response to antigenic stimulus | 0.0213406109698887 |
| GO:0002524 | hypersensitivity | 0.0213406109698887 |
| GO:0000299 | integral to membrane of membrane fraction | 0.0213406109698887 |
| GO:0007162 | negative regulation of cell adhesion | 0.0219975137052059 |
| GO:0042130 | negative regulation of T cell proliferation | 0.0219975137052059 |
| GO:0002861 | regulation of inflammatory response to antigenic stimulus | 0.0219975137052059 |
| GO:0002437 | inflammatory response to antigenic stimulus | 0.0219975137052059 |
| GO:0045061 | thymic T cell selection | 0.0219975137052059 |
| GO:0032640 | tumor necrosis factor production | 0.0230305870421663 |
| GO:0045058 | T cell selection | 0.024429934716648 |
| GO:0002703 | regulation of leukocyte mediated immunity | 0.024429934716648 |
| GO:0002706 | regulation of lymphocyte mediated immunity | 0.024429934716648 |
| GO:0050868 | negative regulation of T cell activation | 0.0246732476426524 |
| GO:0008624 | induction of apoptosis by extracellular signals | 0.0246732476426524 |
| GO:0002697 | regulation of immune effector process | 0.0246732476426524 |
| GO:0050672 | negative regulation of lymphocyte proliferation | 0.0246732476426524 |
| GO:0032945 | negative regulation of mononuclear cell proliferation | 0.0246732476426524 |
| GO:0002819 | regulation of adaptive immune response | 0.027501868906009 |
| GO:0002822 | regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. | 0.027501868906009 |
| GO:0033077 | T cell differentiation in the thymus | 0.0301260709408571 |
| GO:0051250 | negative regulation of lymphocyte activation | 0.0301260709408571 |
| GO:0042102 | positive regulation of T cell proliferation | 0.0319583419061254 |
| GO:0031347 | regulation of defense response | 0.0326021990965578 |
| GO:0051241 | negative regulation of multicellular organismal process | 0.0326021990965578 |
| GO:0050727 | regulation of inflammatory response | 0.0326021990965578 |
| GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0353734580124094 |
| GO:0032946 | positive regulation of mononuclear cell proliferation | 0.0385149164805372 |
| GO:0050671 | positive regulation of lymphocyte proliferation | 0.0385149164805372 |
| GO:0045727 | positive regulation of translation | 0.0421072289428701 |
| GO:0042129 | regulation of T cell proliferation | 0.0432242556945791 |
| GO:0050870 | positive regulation of T cell activation | 0.0432242556945791 |
| GO:0031328 | positive regulation of cellular biosynthetic process | 0.0432242556945791 |
| GO:0048583 | regulation of response to stimulus | 0.0435742622990178 |
| GO:0030155 | regulation of cell adhesion | 0.0439139104015371 |
| GO:0009615 | response to virus | 0.0471136079639364 |
| GO:0042035 | regulation of cytokine biosynthetic process | 0.0473928022269503 |
| GO:0050670 | regulation of lymphocyte proliferation | 0.0481839177904082 |
| GO:0032944 | regulation of mononuclear cell proliferation | 0.0481839177904082 |
| GO:0009891 | positive regulation of biosynthetic process | 0.0481839177904082 |
| GO:0042098 | T cell proliferation | 0.0486756628513152 |
| GO:0005625 | soluble fraction | 0.0486756628513152 |
Relative expression of the co-expression cluster over median <br>Analyst:
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic cell | 7.77e-12 | 32 |
| hematopoietic oligopotent progenitor cell | 7.77e-12 | 32 |
| hematopoietic stem cell | 7.77e-12 | 32 |
| angioblastic mesenchymal cell | 7.77e-12 | 32 |
| hematopoietic multipotent progenitor cell | 7.77e-12 | 32 |
| hematopoietic lineage restricted progenitor cell | 9.24e-09 | 25 |
| common myeloid progenitor | 6.29e-07 | 19 |
| lymphoid lineage restricted progenitor cell | 8.08e-07 | 12 |
| Ontology term | p-value | n |
|---|---|---|
| hemolymphoid system | 9.15e-17 | 48 |
| immune system | 9.15e-17 | 48 |
| hematopoietic system | 2.30e-15 | 45 |
| blood island | 2.30e-15 | 45 |
| hemopoietic organ | 3.67e-11 | 29 |
| immune organ | 3.67e-11 | 29 |
| mixed endoderm/mesoderm-derived structure | 2.90e-09 | 35 |
| thymus | 1.50e-08 | 23 |
| neck | 1.50e-08 | 23 |
| respiratory system epithelium | 1.50e-08 | 23 |
| hemolymphoid system gland | 1.50e-08 | 23 |
| pharyngeal epithelium | 1.50e-08 | 23 |
| thymic region | 1.50e-08 | 23 |
| pharyngeal gland | 1.50e-08 | 23 |
| entire pharyngeal arch endoderm | 1.50e-08 | 23 |
| thymus primordium | 1.50e-08 | 23 |
| early pharyngeal endoderm | 1.50e-08 | 23 |
| pharynx | 4.55e-08 | 24 |
| gland of gut | 4.55e-08 | 24 |
| upper respiratory tract | 4.55e-08 | 24 |
| chordate pharynx | 4.55e-08 | 24 |
| pharyngeal arch system | 4.55e-08 | 24 |
| pharyngeal region of foregut | 4.55e-08 | 24 |
| lateral plate mesoderm | 1.22e-07 | 87 |
| respiratory tract | 4.25e-07 | 41 |
| respiratory system | 7.84e-07 | 42 |
| mesoderm | 9.15e-07 | 120 |
| mesoderm-derived structure | 9.15e-07 | 120 |
| presumptive mesoderm | 9.15e-07 | 120 |
TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.400153 |
| MA0004.1 | 0.434673 |
| MA0006.1 | 0.271714 |
| MA0007.1 | 0.419994 |
| MA0009.1 | 0.870101 |
| MA0014.1 | 0.0611475 |
| MA0017.1 | 1.46217 |
| MA0019.1 | 0.688051 |
| MA0024.1 | 0.826339 |
| MA0025.1 | 1.10341 |
| MA0027.1 | 2.51754 |
| MA0028.1 | 0.281528 |
| MA0029.1 | 0.804619 |
| MA0030.1 | 0.811181 |
| MA0031.1 | 0.775627 |
| MA0038.1 | 0.577528 |
| MA0040.1 | 0.882616 |
| MA0041.1 | 0.360875 |
| MA0042.1 | 0.348174 |
| MA0043.1 | 0.966833 |
| MA0046.1 | 0.906029 |
| MA0048.1 | 0.102483 |
| MA0050.1 | 0.472794 |
| MA0051.1 | 0.586414 |
| MA0052.1 | 0.890676 |
| MA0055.1 | 0.523649 |
| MA0056.1 | 0 |
| MA0057.1 | 0.643187 |
| MA0058.1 | 0.341628 |
| MA0059.1 | 0.353484 |
| MA0060.1 | 0.574356 |
| MA0061.1 | 0.638933 |
| MA0063.1 | 0 |
| MA0066.1 | 0.566617 |
| MA0067.1 | 1.21448 |
| MA0068.1 | 1.61305 |
| MA0069.1 | 0.891016 |
| MA0070.1 | 0.881319 |
| MA0071.1 | 0.471969 |
| MA0072.1 | 0.872842 |
| MA0073.1 | 1.38205 |
| MA0074.1 | 1.31555 |
| MA0076.1 | 0.315013 |
| MA0077.1 | 0.851175 |
| MA0078.1 | 0.61926 |
| MA0081.1 | 0.980744 |
| MA0083.1 | 0.96604 |
| MA0084.1 | 1.54225 |
| MA0087.1 | 0.922929 |
| MA0088.1 | 0.49616 |
| MA0089.1 | 0 |
| MA0090.1 | 0.401197 |
| MA0091.1 | 0.447561 |
| MA0092.1 | 0.401504 |
| MA0093.1 | 0.289361 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.519598 |
| MA0101.1 | 0.362124 |
| MA0103.1 | 0.307078 |
| MA0105.1 | 0.823589 |
| MA0106.1 | 0.626997 |
| MA0107.1 | 0.301222 |
| MA0108.2 | 0.710846 |
| MA0109.1 | 0 |
| MA0111.1 | 1.06639 |
| MA0113.1 | 0.598933 |
| MA0114.1 | 0.222763 |
| MA0115.1 | 0.969632 |
| MA0116.1 | 1.36991 |
| MA0117.1 | 0.937363 |
| MA0119.1 | 0.362692 |
| MA0122.1 | 0.957212 |
| MA0124.1 | 1.16127 |
| MA0125.1 | 1.0872 |
| MA0130.1 | 0 |
| MA0131.1 | 0.683521 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00325 |
| MA0136.1 | 1.35732 |
| MA0139.1 | 0.506952 |
| MA0140.1 | 0.519484 |
| MA0141.1 | 1.56635 |
| MA0142.1 | 0.761136 |
| MA0143.1 | 0.615203 |
| MA0144.1 | 0.225588 |
| MA0145.1 | 0.246409 |
| MA0146.1 | 0.0169049 |
| MA0147.1 | 0.236889 |
| MA0148.1 | 0.450593 |
| MA0149.1 | 0.367458 |
| MA0062.2 | 0.84271 |
| MA0035.2 | 0.524137 |
| MA0039.2 | 0.589101 |
| MA0138.2 | 0.675599 |
| MA0002.2 | 0.513194 |
| MA0137.2 | 0.32312 |
| MA0104.2 | 0.18504 |
| MA0047.2 | 0.576767 |
| MA0112.2 | 0.90045 |
| MA0065.2 | 0.528619 |
| MA0150.1 | 0.419883 |
| MA0151.1 | 0 |
| MA0152.1 | 0.576873 |
| MA0153.1 | 1.01988 |
| MA0154.1 | 0.677425 |
| MA0155.1 | 0.0804339 |
| MA0156.1 | 0.843735 |
| MA0157.1 | 0.729116 |
| MA0158.1 | 0 |
| MA0159.1 | 0.246253 |
| MA0160.1 | 0.453546 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0925951 |
| MA0163.1 | 0.991519 |
| MA0164.1 | 0.551114 |
| MA0080.2 | 2.26 |
| MA0018.2 | 0.560731 |
| MA0099.2 | 0.669311 |
| MA0079.2 | 0.837555 |
| MA0102.2 | 1.59466 |
| MA0258.1 | 0.60477 |
| MA0259.1 | 0.227035 |
| MA0442.1 | 0 |
